Long-term CO_2 emission analyses on the energy structure in Japan were conducted using the MARKAL. The MARKAL model is one of analysis tools to evaluate the long-term change of energy system in a country, and is composed of energy resources, energy supply technologies, energy ultimate demand technologies and energy service demands with them connected by energy carriers. This paper presents the analyses investigating energy structure at house and effects of CO_2 capture and storage (CCS) until 2050. It was shown that the usage of electricity and gas is strongly affected by the investment costs, and the large reduction is needed for CGS widespread use. The results also showed that the CCS is effective in the case that the installed capacity of nuclear power plant, and the effective capture of CO_2 reduces the social costs for the reduction of CO_2 emission.